Maybe it has been said before, if so, sorry (I've just found the time to read the top 60 comments) ...
First off, nice design. I like it. It will certainly require some getting-used-to (I still like the old logo better -- but that's probably just me :)
The page renders fine in IE 5.5 and Netscape 4.7x, but it has a flaw in Opera 5 : The logo is cut in two : the part that's in the topic-bar is about a line off from the rest of the logo. <br />
Come to think of it, the title bar does not fit on an 80x24 terminal with links (that text-mode browser with tables, frames, mouse-support and whatnot, not lynx), the topic-bar causes the page to render wider than one screen which is a little distracting (the stories and sidebars are ok, however). This also happens with 111 columns but is ok on 132 ;) Not that I would _ever_ compare to that other site, but it doesn't happen there ;-)
Also, it might be a good idea to run this page through http://validator.w3.org some time. Yes, I know almost no page really complies, but it never hurts to make some adjustments to remain closely compliant to the standards _if it does not render the page unrenderable on most browsers_ :)
I would like it if it was possible to decide whether one had the +/- buttons the old way or the new way -- When I'm not logged in the page looks a _lot_ nicer to me compared to when I'm logged in. Those buttons just seem to clutter the page or distract from my reading, I can't exactly pinpoint what exactly it is.
Somebody else already proposed to put the Everything link into the middle of the bar instead of at the left. Personally I'd prefer it to stay this way since it is more easily reached with the keyboard than the alternative.
That about sums up my suggestions for the new layout ...
Thanks for it, it really looks cleaner than the old one. Whether it is better is a matter up for discussion, I think yes, others think no. Guess that's just the way the world works :)
Oh, and don't forget to sleep. It helps. :)
men are reasoning, not reasonable animals.